[Bio-linux-devel] 16.04.1 Upgrade Follies

[Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas]

Hi Tony,

Just would like to say I'm anxiously waiting for this next release!

Although I have to confess that I already got bored of Xenial and upgraded
to Zesty Zapus this week. :D

Kind Regards,

_____________________________________________

Raony Guimarães Corrêa Do Carmo Lisboa Cardenas
PhD in Bioinformatics

email: raonyguimaraes at gmail.com
skype/hangouts: raonyguimaraes
phone: +48 722 148 478
_____________________________________________

On Wed, Nov 2, 2016 at 3:42 PM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 02/11/16 14:19, mckennep at mskcc.org wrote:
> > Hi,
> >
> > I made a stupid mistake and tried to upgrade to Ubuntu 16.04.1 on a
> > Bio-Linux 8 installation.
>
> Hi, Peter.
>
> You didn't make a stupid mistake trying the upgrade!
>
> I've got Bio-Linux 8 running under Ubuntu 16.04 LTS on my laptop. A few
> things are terminally broken (e.g. Galaxy in particular). I've
> work-arounds for some packages, but more work needs to be done before I
> make a Bio-Linux 9 release based on Ubuntu 16.04.
>
> > Now, after starting grub, I get a black screen with the following
> > (xxx = large number):
> >
> > lvmetad is not active yet, using direct activation during sysinit
> > /dev/mapper/biolinux--vg-root: recovering journal
> > /dev/mapper/biolinux--vg-root: clean, xxxxxxx/xxxxxxxx files,
> > xxxxxx/xxxxxxx blocks
> >
> > I searched and found this:
> >
> > http://askubuntu.com/questions/769863/lvmetad-is-
> not-active-yet-using-direct-activation-during-sysinit/783977#783977
> >
> >  ...but those suggestions didn't work for me.  Adding 'nomodeset'
> > after 'quiet splash' in the startup commands gives me the same black
> > screen with the 'lvmetad' error message, but now I also get the
> > Biolinux8 green startup dots cycling on the screen forever.
> >
> > I looked up what lvmetad is, but I don't really understand what it
> > does. Any ideas?
>
> The BIG mistake you made was using LVM :-(
>
> If you want to run Bio-Linux on a server, use "md" RAID instead of LVM.
> You don't need LVM on a laptop or desktop anyway, but you should use
> "md" RAID on a workstation if it has several disks.
>
> What you need to do is fix your broken LVM from the command-line!
>
> HTH,
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
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